A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

Abstract

Background Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology. Results Our results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens. Conclusions This study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

“…In that case, a 4.3 kb block of sequences upstream of the gene was inverted in strain 1306 compared to strain 618, moving the transcription start site active in strain 618 away from the gene in strain 1306. These rearrangements appear to be recent events since they were not observed in other sequenced strains including T30-4, 88069, KR-1, and RC1-10 [51,52]. When all of the silent genes in 1306 and 618 were examined, we discovered that overall they were much more likely to belong to a family (defined by OrthoMCL [53]) than those expressed in both strains (P<10 −4 ; Fig 8F).…”

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

“…Beyond adding genomes to the graphs, a step further would be to create a pangenome graph that incorporates fully phased diploid or polyploid genome assemblies, thus uncovering possible variation and recombination between haplotypes (Henningsen et al ., 2024). For example, oomycetes are mostly diploids, but there are various reports of whole-genome duplication in Phytophthora betacei , and aneuploidy in Phytophthora capsici and in Phytophthora cinnamomi (Seidl et al ., 2012; Kasuga et al ., 2016; Hu et al ., 2020; Ayala-Usma et al ., 2021; Engelbrecht et al ., 2021). We therefore anticipate that pangenomic approaches will be instrumental to uncover the full extent of genomic variation in filamentous plant pathogens (Sirén et al ., 2021; Garcia et al ., 2024), which, in turn, will unveil new theories about their emergence and evolution, impacting our ability to predict and manage plant diseases.…”

The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes

“…This is consistent with the previously reported correlation of repeat content with genome size across multiple oomycete species, including downy mildews [18]. Inflation of genome size exclusively by retention of transposable elements is different from some Phytophthora spp., where whole-genome duplication in addition to proliferation of transposable elements have resulted in an increased genome sizes [23, 24].…”